PLUMED-NEST

Project ID: plumID:22.013
Source: plumed/apo/analysis/plumed.c-c_distance.dat
Originally used with PLUMED version: 2.5
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr

Click on the labels of the actions for more information on what each action computes

MOLINFO
This command is used to provide information on the molecules that are present in your system. More details
 
STRUCTURE
a file in pdb format containing a reference structure
=reference.pdb 
MOLTYPE
 what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible
=rna
WHOLEMOLECULES
This action is used to rebuild molecules that can become split by the periodic boundary conditions. More details
 
ENTITY0
the atoms that make up a molecule that you wish to align
=1-1062

d_1C_2U: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=21,51
The DISTANCE action with label d_1C_2U calculates a scalar quantityd_2U_3G: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=51,81
The DISTANCE action with label d_2U_3G calculates a scalar quantityd_3G_4G: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=81,115
The DISTANCE action with label d_3G_4G calculates a scalar quantityd_4G_5G: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=115,149
The DISTANCE action with label d_4G_5G calculates a scalar quantityd_5G_6U: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=149,183
The DISTANCE action with label d_5G_6U calculates a scalar quantityd_6U_7C: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=183,214
The DISTANCE action with label d_6U_7C calculates a scalar quantityd_7C_8G: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=214,244
The DISTANCE action with label d_7C_8G calculates a scalar quantityd_8G_9C: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=244,279
The DISTANCE action with label d_8G_9C calculates a scalar quantityd_9C_10A: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=279,310
The DISTANCE action with label d_9C_10A calculates a scalar quantityd_10A_11G: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=310,342
The DISTANCE action with label d_10A_11G calculates a scalar quantityd_11G_12U: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=342,376
The DISTANCE action with label d_11G_12U calculates a scalar quantityd_12U_13A: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=376,407
The DISTANCE action with label d_12U_13A calculates a scalar quantityd_13A_14A: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=407,440
The DISTANCE action with label d_13A_14A calculates a scalar quantityd_14A_15C: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=440,473
The DISTANCE action with label d_14A_15C calculates a scalar quantityd_15C_16C: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=473,504
The DISTANCE action with label d_15C_16C calculates a scalar quantityd_16C_17C: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=504,535
The DISTANCE action with label d_16C_17C calculates a scalar quantityd_17C_18C: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=535,566
The DISTANCE action with label d_17C_18C calculates a scalar quantityd_18C_19A: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=566,597
The DISTANCE action with label d_18C_19A calculates a scalar quantityd_19A_20G: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=597,629
The DISTANCE action with label d_19A_20G calculates a scalar quantityd_20G_21U: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=629,663
The DISTANCE action with label d_20G_21U calculates a scalar quantityd_21U_22U: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=663,693
The DISTANCE action with label d_21U_22U calculates a scalar quantityd_22U_23A: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=693,724
The DISTANCE action with label d_22U_23A calculates a scalar quantityd_23A_24A: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=724,757
The DISTANCE action with label d_23A_24A calculates a scalar quantityd_24A_25C: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=757,790
The DISTANCE action with label d_24A_25C calculates a scalar quantityd_25C_26A: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=790,821
The DISTANCE action with label d_25C_26A calculates a scalar quantityd_26A_27A: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=821,854
The DISTANCE action with label d_26A_27A calculates a scalar quantityd_27A_28A: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=854,887
The DISTANCE action with label d_27A_28A calculates a scalar quantityd_28A_29A: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=887,920
The DISTANCE action with label d_28A_29A calculates a scalar quantityd_29A_30C: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=920,953
The DISTANCE action with label d_29A_30C calculates a scalar quantityd_30C_31A: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=953,984
The DISTANCE action with label d_30C_31A calculates a scalar quantityd_31A_32A: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=984,1017
The DISTANCE action with label d_31A_32A calculates a scalar quantityd_32A_33G: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1017,1049

The DISTANCE action with label d_32A_33G calculates a scalar quantity
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
 
STRIDE
 the frequency with which the quantities of interest should be output
=1 
FILE
the name of the file on which to output these quantities
=consecutive_c2_distance